Typing tool

Complete norovirus genomes

JQ613572  GII.4 Den Haag
 GII.P4 Den Haag

Length: 7,560 | 3 CDS

ORF1: 5..5104
ORF2: 5085..6707
ORF3: 6707..7513
LOCUS       JQ613572                7560 bp    RNA     linear   VRL 10-MAY-2013
DEFINITION  Norovirus Hu/GII.4/StVincents/NSW217I/2010/AU non-structural
            polyprotein, VP1, and VP2 genes, complete cds.
ACCESSION   JQ613572
VERSION     JQ613572.1
KEYWORDS    .
SOURCE      Norovirus Hu/GII.4/StVincents/NSW217I/2010/AU
  ORGANISM  Norovirus Hu/GII.4/StVincents/NSW217I/2010/AU
            Viruses; Riboviria; Orthornavirae; Pisuviricota; Pisoniviricetes;
            Picornavirales; Caliciviridae; Norovirus.
REFERENCE   1  (bases 1 to 7560)
  AUTHORS   Eden,J.S., Tanaka,M.M., Boni,M.F., Rawlinson,W.D. and White,P.A.
  TITLE     Recombination within the Pandemic Norovirus GII.4 Lineage
  JOURNAL   J. Virol. 87 (11), 6270-6282 (2013)
   PUBMED   23536665
REFERENCE   2  (bases 1 to 7560)
  AUTHORS   Eden,J.-S. and White,P.A.
  TITLE     Direct Submission
  JOURNAL   Submitted (03-FEB-2012) School of Biotechnology and Biomolecular
            Sciences, University of New South Wales, Anzac Parade, Sydney, NSW
            2052, Australia
COMMENT     ##Assembly-Data-START##
            Sequencing Technology :: Sanger dideoxy sequencing
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..7560
                     /organism="Norovirus Hu/GII.4/StVincents/NSW217I/2010/AU"
                     /mol_type="genomic RNA"
                     /strain="Hu/GII.4/StVincents/NSW217I/2010/AU"
                     /host="Homo sapiens"
                     /db_xref="taxon:1183313"
                     /country="Australia"
                     /collection_date="Apr-2010"
                     /note="genotype: GII.4"
     5'UTR           1..4
     CDS             5..5104
                     /note="ORF1"
                     /codon_start=1
                     /product="non-structural polyprotein"
                     /protein_id="AFJ21450.1"
                     /translation="MKMASNDASAAAVANSNNDTAKSSNDKMFSNMAVTLKRALGARP
                     KQPPPREIPQRPPRPPTPELVKKIPPPPPNGEDDVVVSYSAKDGVSGLPELSTVRQPE
                     ETSTAFSVPPLNQRENRDAKEPLTGTILEMWDGEIYHYGLYVERGLVLGVHKPPAAIS
                     LAKVELTPLSLFWRPVYTPQYLISPDTLKKLHGETFPYTAFDNNCYAFCCWVLDLNDS
                     WLSRRMIQRTTGFFRPYQDWNRKPLPTMDDSKLKKVANIFLCALSSLFTRPIKDIIGK
                     LRPLNIINILASCDWTFAGIVESLILLAELFGVFWTPPDVSAMIAPLLGDFELQGPED
                     LVVELVPVVMGGIGLVLGFTKEKIGKMLSSAASTLRACKDLGAYGLEILKLVMKWFFP
                     KKEEANELAMVRSIEDAVLDLEAIENNHMTTLLKDKDSLATYMRTLDLEEEKARKLST
                     KSASPDIVGTINALLARIAAARSLVHRAKEELSSRPRPVVLMISGRPGIGKTHLAREV
                     AKRIAASLTGDQRVGLIPRNGVDHWDAYKGERVVLWDDYGMSNPIHDALRLQELADTC
                     PLTLNCDRIENKGKVFDSDVIIITTNLANPAPLDYVNFEACSRRIDFLVYAEAPEVEK
                     AKRDFPGQPDMWKNAFSSDFSHIKLALAPQGGFDKNGNTPHGKGVMKTLTTGSLIARA
                     SGLLHERLDEFELQGPALTTFNFDRNKVLAFRQLAAENKYGLMDTMKVGRQLKDVRTM
                     PELKQALKNISIKKCQIVYSGCTYTLESDGKGNVKVDRVQSTSVQTNNELAGALHHLR
                     CARIRYYVKCVQEALYSIIQIAGAAFVTTRIIKRVNIQDLWSKPQVENTEEATSKDGC
                     PKPKDDEEFVVSSDDIKTEGKKGKNKTGRGKKHTAFSSKGLSDEEYDEYKRIREERNG
                     KYSIEEYLQDRDKYYEEVAIARATEEDFCEEEEAKIRQRIFRPTRKQRKEERASLGLV
                     TGSEIRKRNPEDFKPKGKLWADDDRSVDYNEKLSFEAPPSIWSRIVNFGSGWGFWVSP
                     SLFITSTHVIPQGAKEFFGVPIKQIQVHKSGEFCRLRFPKPIRTDVTGMILEEGAPEG
                     TVVTLLIKRSTGELMPLAARMGTHATMKIQGRTVGGQMGMLLTGSNAKSMDLGTTPGD
                     CGCPYIYKRGNDYVVIGVHTAAARGGNTVICATQGGEGEATLEGGDSKGTYCGAPILG
                     PGSAPKLSTKTKFWRSSTAPLPPGTYEPAYLGGKDPRVKGGPSLQQVMRDQLKPFTEP
                     RGKPPKPSVLEAAKKTIINVLEQTIDPPEKWSFAQACASLDKTTSSGHPHHMRKNDCW
                     NGESFTGKLADQASKANLMFEEGKNMTPVYTGALKDELVKTDKIYGKIKKRLLWGSDL
                     ATMIRCARAFGGLMDELKAHCVTLPVRVGINMNEDGPIIFEKHSRYRYHYDADYSRWD
                     STQQRAVLAAALEIMVKFSSEPHLAQVVAEDLLSPSVVDVGDFTISINEGLPSGVPCT
                     SQWNSIAHWLLTLCALSEVTNLSPDIIQANSLFSFYGDDEIVSTDIKLDPEKLTAKLK
                     EYGLKPTRPDKTEGPLVISEDLDGLTFLRRTVTRDPAGWFGKLEQSSILRQMYWTRGP
                     NHEDPSESMIPHSQRPIQLMSLLGEAALHGPTFYSKISKLVIAELKEGGMDFYVPRQE
                     SMFRWMRFSDLSTWEGDRNLAPSFVNEDGVE"
     CDS             5085..6707
                     /note="major capsid protein"
                     /codon_start=1
                     /product="VP1"
                     /protein_id="AFJ21451.1"
                     /translation="MKMASNDANPSDGSAANLVPEVNNEVMALEPVVGAAIAAPVAGQ
                     QNVIDPWIRNNFVQAPGGEFTVSPRNAPGETLWSAPLGPDLNPYLSHLARMYNGYAGG
                     FEVQVILAGNAFTAGKIIFAAVPPNFPTEGLSPSQVTMFPHIIVDVRQLEPVLIPLPD
                     VRNNFYHYNQSNDSTIKLIAMLYTPLRANNAGDDVFTVSCRVLTRPSPDFDFIFLVPP
                     TVESRTKPFTVPILTVEEMTNSRFPIPLEKLFTGPSSAFVVQPQNGRCTTDGVLLGTT
                     QLSPVNICTFRGDVTHIAGSRNYTMNLASLNWNNYDPTEEIPAPLGTPDFVGKIQGML
                     TQTTQGDGSTRGHKATVYTGSADFTPKLGSVQFATDTENDFETHQNTKFTPVGVIQDG
                     STTHRNEPQQWALPSYSGRSAHNVHLAPAVAPNFPGEQLLFFRSTMPGCSGYPNMDLD
                     CLLPQEWVQHFYQEAAPAQSDVALLRFVNPDTGRVLFECKLHKSGYVTVAHTGQHDLV
                     IPPNGYFRFDSWVNQFYTLAPMGNGTGRRRAL"
     CDS             6707..7513
                     /note="minor structural protein"
                     /codon_start=1
                     /product="VP2"
                     /protein_id="AFJ21452.1"
                     /translation="MAGAFFAGLASDVLSSGLGSLINAGAGAINQKIDFENNRKLQQA
                     SFQFSSNLQQASFQHDKEMLQAQIEATKKLQQEMMKVKQAMLLEGGFFETDAARGAIN
                     APMTKALDWSGTRYWAPDARITTYNAGRFSTPQPSGALPGRINPRNPTPARGSPSISS
                     NASIATSIYSNQTVSTRLGSTAGSGTNVSSLPSTARTRSWVEDQNRNLSPFMRGAHNM
                     SFVTPPSSRSSSQGTVSTVPKDVLDSWTGAFNTRRQPLFAHIRRRGESRV"
     3'UTR           7514..7560
ORIGIN      
        1 gtgaatgaag atggcctcta acgacgcttc cgctgccgct gttgctaaca gcaacaacga
       61 caccgcaaaa tcttcaaatg acaaaatgtt ttctaacatg gctgtcactc ttaaacgggc
      121 cctcggggcg cggcctaaac agcccccccc gagggaaata ccacaaaggc ccccacgacc
      181 acctactcca gaactggtca aaaagatccc tcctcccccg cccaacggag aggatgatgt
      241 agtggtttct tatagtgcca aagacggcgt ttccggtttg cctgagcttt ccaccgtcag
      301 gcaaccggaa gaaaccagta cggccttcag cgtccctcca ctcaatcaga gggagaatag
      361 ggatgctaag gaaccactga ctgggacaat tctggaaatg tgggatggag aaatctacca
      421 ttatggcctg tatgttgagc gaggtcttgt gctgggtgta cacaaaccac cagctgccat
      481 tagtctcgcc aaggtcgaat taacaccact ctccttgttc tggagacctg tgtacactcc
      541 tcagtacctc atttctccag acactctcaa gaagttacac ggagaaacat ttccctacac
      601 agcctttgac aacaactgct atgccttttg ttgctgggtc ctggatttaa acgactcgtg
      661 gctgagtagg agaatgatcc agagaacaac tggcttcttc agaccctacc aagattggaa
      721 taggaaaccc ctccccacta tggatgattc caaattgaag aaggtagcta acatattcct
      781 gtgtgccctg tcttcgctat tcaccaggcc cataaaagac ataataggaa agttaaggcc
      841 tctcaacatc atcaacatcc tggcttcatg tgattggact ttcgcaggca tagtggagtc
      901 cttgatactc ttggcagagc tctttggagt cttctggaca cccccagatg tgtctgcgat
      961 gattgccccc ttactcggtg attttgagtt acaaggacct gaggaccttg tagtggagct
     1021 cgtccctgta gtgatggggg ggattggttt ggtgctagga ttcaccaaag agaagattgg
     1081 aaaaatgttg tcatctgctg catccacctt aagagcttgc aaagaccttg gtgcatatgg
     1141 gctagagatc ctaaagttag tcatgaagtg gttcttcccg aagaaagagg aagcgaatga
     1201 actggctatg gtgagatcca tcgaggatgc agtactggac cttgaggcaa ttgaaaacaa
     1261 ccatatgacc accttgctca aagacaaaga cagcctggca acctacatga gaacccttga
     1321 cctcgaggaa gagaaagcca gaaaactctc aaccaagtct gcttcacctg acatcgtggg
     1381 cacaatcaac gcacttctgg cgagaatcgc cgctgcacgc tccctggtgc accgagcgaa
     1441 ggaggagctt tccagcagac caagacctgt agtcttgatg atatcaggca ggccaggaat
     1501 agggaagacc caccttgcca gggaagtggc taagagaatc gcagcctccc tcacaggaga
     1561 ccagcgtgta ggcctcatcc cacgcaatgg cgtcgatcac tgggatgcgt acaaggggga
     1621 gagggtcgtc ctatgggacg actacggaat gagcaatccc atccacgacg ccctcaggct
     1681 gcaagaactc gctgacactt gccccctcac cctaaattgt gacaggattg agaataaagg
     1741 aaaggtcttt gacagcgatg tcatcattat cactactaac ctggccaacc cagcaccact
     1801 ggactatgtc aactttgaag catgctcgag gcgcatcgat ttcctcgtgt acgcagaggc
     1861 ccccgaggtc gaaaaggcga agcgcgactt cccgggccag cctgacatgt ggaaaaacgc
     1921 ttttagttct gatttctcac acataaaatt ggcactagct ccacaaggtg gctttgataa
     1981 gaatgggaac accccacacg ggaagggcgt catgaagact ctcaccactg gctccctcat
     2041 tgcccgggca tcagggctgc ttcatgagag attggatgag tttgaactac agggcccagc
     2101 tctcaccacc tttaactttg accgcaacaa agtgcttgcc ttcagacagc ttgctgctga
     2161 aaacaaatat gggttgatgg acacaatgaa agttgggagg cagctcaagg atgtcagaac
     2221 catgccagaa cttaaacaag cactcaagaa tatctcaatc aagaagtgcc agattgtgta
     2281 cagtggttgc acatacacac ttgagtctga tggcaagggc aatgtgaaag ttgacagagt
     2341 tcagagtacc tccgttcaga ccaacaatga gttggctggc gccctgcacc atctaaggtg
     2401 cgccagaatc aggtattatg ttaagtgtgt tcaggaggcc ctgtattcta tcatccagat
     2461 tgctggggct gcatttgtca ccacgcgcat catcaagcgt gtgaacattc aagacttatg
     2521 gtccaagcca caagtggaaa acacagagga ggctaccagc aaggacgggt gcccaaaacc
     2581 caaagatgat gaggagttcg tcgtttcatc tgacgacatt aaaactgagg gtaagaaagg
     2641 gaagaacaag actggccgcg gcaagaagca cacagccttc tcaagtaaag gtctcagtga
     2701 tgaagagtat gacgagtaca agagaattag agaggaaagg aatggcaagt actccataga
     2761 agagtacctt caggacaggg acaaatatta tgaggaggtg gccattgcca gggcgaccga
     2821 ggaagacttc tgtgaagagg aggaggccaa gatccggcaa aggatcttca gaccaacaag
     2881 gaagcaacgc aaggaagaaa gggcttctct cggtttagtc acaggttctg aaattaggaa
     2941 aagaaatcca gaagacttca agcccaaggg gaaactatgg gctgacgatg acagaagtgt
     3001 ggactacaat gaaaaactca gttttgaggc cccaccaagc atctggtcaa ggatagtcaa
     3061 ctttggctca ggttggggct tctgggtctc ccccagcctg ttcataacat caacccacgt
     3121 cataccccag ggcgcaaagg agttctttgg agtccccatc aaacaaattc aggtgcacaa
     3181 gtcaggcgaa ttctgtcgct tgaggttccc aaaaccaatc aggactgatg tgactggcat
     3241 gatcttggag gaaggtgccc ccgaaggcac cgtagtcaca ctactcatca aaaggtctac
     3301 tggagaactc atgcccctag cagctagaat gggaacccac gcaaccatga aaattcaagg
     3361 gcgcactgtt ggaggtcaga tgggcatgct tctgacagga tccaacgcca aaagcatgga
     3421 tctgggcacc acaccaggtg attgcggctg tccctacatc tacaagagag gaaacgacta
     3481 tgtagtcatt ggagtccaca cggctgccgc tcgtggggga aacactgtca tatgtgccac
     3541 ccaggggggt gaaggggaag ctacacttga aggtggtgac agtaagggaa catactgtgg
     3601 tgcaccaatc ctaggcccag ggagtgcccc aaaactcagc accaaaacca aattctggag
     3661 atcatccaca gcaccactcc cacctggcac ctatgaacca gcctaccttg gtggcaaaga
     3721 ccccagagtc aagggtggcc cctcgttgca gcaagtcatg agggaccagc tgaaaccatt
     3781 tacagagcct aggggtaagc caccaaagcc aagtgtgtta gaagctgcca agaaaaccat
     3841 catcaatgtc cttgaacaga caattgaccc acctgagaag tggtcgttcg cacaagcttg
     3901 cgcgtccctt gataagacca cttctagcgg ccatccgcac cacatgcgga aaaacgactg
     3961 ctggaacggg gagtccttca caggcaagct ggcagaccag gcttccaagg ccaacctgat
     4021 gtttgaagaa gggaagaaca tgaccccagt ctacacaggt gcacttaagg atgaattagt
     4081 caaaactgac aaaatttatg gcaagatcaa gaagaggctt ctctggggct cggatttggc
     4141 aaccatgatc cggtgtgctc gagcattcgg aggtctgatg gatgaactca aagcacactg
     4201 tgtcacactc cctgtcagag ttggtataaa tatgaatgag gatggcccca tcatcttcga
     4261 gaagcattcc aggtacagat accactatga tgctgattac tctcggtggg attcaacaca
     4321 acagagagcc gtgctggcag ctgctctaga aatcatggtt aaattctcct cagaaccaca
     4381 tttggctcag gtagtagcag aagaccttct ttctcctagc gtagtggatg tgggtgactt
     4441 cacaatatca atcaacgagg gtcttccctc tggggtgccc tgcacctccc aatggaactc
     4501 tatcgcccac tggcttctca ctctctgtgc actctccgaa gtcacaaatt tgtctccaga
     4561 catcatacag gctaattctc tcttctcctt ctatggtgat gatgaaattg ttagtacaga
     4621 cataaaatta gacccagaga agttgacggc aaagcttaag gaatatgggt tgaaaccaac
     4681 ccgccctgac aaaactgaag ggcctcttgt tatttctgaa gacttagacg gtttgacttt
     4741 cctgcggaga actgtgaccc gcgacccagc tggttggttt ggaaaactgg agcagagctc
     4801 aatactcagg caaatgtact ggactagggg ccccaaccat gaagacccat ctgaatcaat
     4861 gatcccacac tctcaaagac ccatacaatt gatgtcctta ctgggagagg ccgcactcca
     4921 cggcccaaca ttctacagta aaatcagcaa attagtcatt gcagagctaa aagaaggtgg
     4981 catggatttt tacgtgccca ggcaagagtc aatgttcagg tggatgagat tctcggatct
     5041 gagcacgtgg gagggcgatc gcaatctggc tcccagtttt gtgaatgaag atggcgtcga
     5101 atgacgccaa cccatctgat gggtccgcag ccaacctcgt cccagaggtc aacaatgagg
     5161 ttatggcttt ggagcccgtt gtcggtgccg ctattgcggc gcccgtagcg ggccaacaaa
     5221 atgtaattga cccctggatt agaaataatt ttgtacaagc ccctggtggg gagttcacag
     5281 tatcccctag aaacgctcca ggtgaaacat tatggagcgc gcccttaggc cctgacctga
     5341 atccctacct atctcatttg gccagaatgt ataatggtta tgcaggtggt tttgaagtgc
     5401 aagtgatcct cgcggggaac gcgttcaccg ccggaaaaat tatatttgca gcagtcccac
     5461 caaattttcc aactgaaggc ttgagtccca gccaggtcac tatgttcccc catataatag
     5521 tagatgttag acaattggaa cctgtgttga tccccttacc tgatgttagg aataacttct
     5581 atcactataa tcagtcaaat gattctacca ttaaattgat agcaatgctg tatacaccac
     5641 ttagggccaa taatgccggg gatgatgtct tcacagtctc ttgtcgagtc ctcacgaggc
     5701 catcccctga ttttgatttc atatttttgg tgccacctac agttgagtca agaaccaagc
     5761 catttactgt cccaatcttg actgttgaag aaatgaccaa ttcaagattc cccattcctt
     5821 tggaaaaatt gttcacgggt cccagcagtg cctttgttgt tcaaccacaa aatggcaggt
     5881 gcacgactga tggcgtgctc ttaggcacca cccaactgtc tcctgtcaac atctgcacct
     5941 tcagagggga tgtcacccac attgcgggtt ctcgcaatta cacaatgaat ttggcctctc
     6001 taaattggaa caattatgac ccaacagaag aaatcccagc ccctctggga actccagatt
     6061 tcgtgggaaa gatccaaggt atgctcactc aaaccacaca gggagatggc tcgacccggg
     6121 gccataaagc cacagtttac actgggagtg ccgacttcac tccaaagctg ggcagtgttc
     6181 aatttgctac tgatacagaa aatgattttg aaactcacca aaatacaaaa ttcaccccag
     6241 tcggtgtcat ccaggatggt agcaccaccc accgaaatga accccaacaa tgggcgctcc
     6301 caagttattc aggtagaagt gcccataatg tgcacctagc ccctgctgta gcccccaatt
     6361 ttccgggtga acaacttctc ttcttcaggt ccactatgcc cggatgcagc gggtatccca
     6421 acatggattt ggattgccta ctcccccagg agtgggtgca gcacttctac caagaggcag
     6481 ctccagcgca atctgatgtg gctctattga gatttgtgaa tccagacacg ggtagggtct
     6541 tgtttgagtg caaacttcat aaatcaggct atgtcacagt ggctcacacc ggccaacatg
     6601 atttggttat cccccccaat ggttatttta ggtttgattc ctgggttaat cagttctaca
     6661 cacttgctcc catgggaaat ggaacggggc gtagacgtgc tttataatgg ctggagcttt
     6721 ctttgctgga ttggcatctg atgtccttag ctctggactt ggttccctaa tcaatgctgg
     6781 ggctggggct atcaaccaaa agattgattt tgaaaataat agaaaattgc agcaagcctc
     6841 ctttcagttt agcagtaatc tacaacaggc ttccttccaa catgataaag agatgctcca
     6901 agcacaaatt gaggccacta aaaagttaca acaagaaatg atgaaagtta aacaggcaat
     6961 gctcttagaa ggtggattct ttgaaacaga tgcagcccgt ggggcaatca acgcccccat
     7021 gacaaaggct ttggactgga gcggaacaag gtactgggcc cctgatgcta ggattacaac
     7081 atataatgca ggccgctttt ccacccccca accttcgggg gcactgccag gaagaatcaa
     7141 tcccaggaac cctacccccg ctaggggctc ccccagtata tcttccaatg cttctattgc
     7201 tacttctata tattcaaatc aaactgtttc aacgagactt ggttctacag ctggttctgg
     7261 caccaatgtc tcgagtctcc cgtcaactgc aaggactagg agttgggttg aggatcaaaa
     7321 cagaaatttg tcacctttca tgaggggggc tcacaacatg tcgtttgtca ctccaccatc
     7381 tagcagatcc tctagccaag gcacagtctc aaccgtgcct aaagatgttt tggactcctg
     7441 gactggcgct ttcaacacgc gcaggcagcc tctcttcgct cacattcgta ggcgagggga
     7501 gtcacgggtg taatgtgaaa agacaaaatt gattatcttt ccctttcttt agtgtctttt
//